The Falling Lotus
by Tenebrae's Downfall
Summary: Four months after the invasion, the gang travels to upstate to await for their leader's revival after their horrid defeat against the Shredder. In a turn of events, Leonardo finally wakes up from his injuries with troubling questions no one was prepared to deal with. While in the misfits of it all, the lingering drama from home slowly returns.. (OCCs, T-cest, AU-ness included).
1. Prologue

**Hello, I'm new to the TMNT fan fiction so I apologize in advance for any mishaps that I may do with my works. This is just my intake on how I feel the beginning of Season three should've went down in the 2012 series. However, I am a huge fan of the 2003 series, so I will be adding some elements of it to many of my TMNT fan fics. Also, I will be using T-Cest in a couple of my works, but the turtles won't be related as blood brothers, but as foster brothers or brothers-in-arms. So don't spam me on how horrible it is, I'm explaining my reasons behind it so take the time to read it instead of going bananas over it alright? Thank you very much.**

 **So I hope you enjoy my long stand alone and see you guys with the first chapter next week!**

 **x-x**

 **Prologue**

 **x-x**

It's been almost four months since we left our beloved home. The Kraang and Shredder defeated us one by one, and took everything with their mutagen and very advanced foot soldiers. The people of the city were either taken into dimension X after being mutated or slaughtered up into bits without a single care, with blood running throughout the streets and sewer pipes.

When we left our home, we drove through the empty highway that lead to upstate with my father's party van, see all but buildings upon buildings, and trees upon trees. Leonardo remained asleep, even after his horrific fight against the Shredder and his elite soldiers, while we were kept on our toes. Our weapons sharp yet slowly dulling away from lack of use.

Things were different without our leader and Sensei. Donatello felt guilty about the invasion; his once hopeful eyes turned dimming into nothingness, losing its light with each day that went pass. When he wanted too, he would come out of the barn to get food, not saying a word to us other than quick formal talk with hellos and good nights whenever everyone else went to bed. Most of the time though, he stayed in the barn to work on creating all sorts of herbal medicines to heal Leo for when he woke, if he woke up I should say.

Raphael was stood by Leonardo's side. Ever since he came out to all of us as bisexual just days before the invasion began and right after Donatello performed a DNA test to confirm their genetics just only out of curiosity. By the time the results were announced, Raphael eventually confessed his feelings for Leonardo in front of Splinter and soon enough, things were in our warrior's favor with his lingering feelings slowly returned. Everything seemed at peace for all of us, especially for Raphael that was until his lover was defeated by the hands of the enemy. But even now, our wounded warrior kept his lone stool near the bathtub with Leo's navy blue blanket wrapped around him, and waited, waited until he passed out on the floor.

Michelangelo tried to maintain a positive outlook when dealing with the worse. He would help me around the house and prepare meals for Raphael and Donatello when they didn't want to be bothered that day. Deep down though, Casey and I knew that he was hurting, but regardless of it, he wanted to keep everyone happy as much as he can for their sanity. And mostly for his own sanity so he won't suffer as well. As for Casey and I? Well, we were in the dark with the 'brothers', trying our best to keep everything at a small level of normalcy when things gotten rough with the constant fights between the warrior and the genius.

But most of all, Master Splinter's fate was worse compare to ours, well expect for Leonardo's. He remained in New York City, unknown to us if he made it out alive after the terrible fight against his old rival. We wanted to stay and fight back, but his orders were final once we saw him falling into the water hole.

It only took us moments to figure out that he was most likely dead to the world when the Shredder gave our beloved sensei a weird gaze of remorse. In the end, we still keep our hopes up that he somehow made it out alive. After all, we all did, just barely.

I wish things were normal again. I wish I can see and hold my dad close again and for the brothers-in-arms to be together instead of broken. But at this point, all we can do is hope.

Right?


	2. Chapter One

Thank you for taking the time for reading " _The Falling Lotus"_ thus far, it means a lot to me and I hope you will enjoy the future installments to it. This is the first time I've ever written outside of the paranormal/fantasy genre and I hope to keep going with it.

 **Warning:** OOC-ness from set characters, AU-ness, and graphic language, violence, and sexual content, 't-cest' (turtles are not biologically related in this story.)

 **Disclaimer:** I don't own anything TMNT related, it rightfully belongs to their creator. I only own Oshiro, Riku, Takuya, Kenji, Hibiki, and Minoru. They're the main occs I will place in my TMNT fan fic universe unless stated otherwise. :)

* * *

 **Chapter One**

* * *

Raphael sat down at the floor in the bathroom that kept his mate protected from the dangers of the outside world. He held the blanket close to him, it along with the lone photograph of his once pet turtle Spike was all Raphael brought with him once he left their sewer home in the city. Raphael wanted to take on the world and defeat the Shredder once and for all, but in the end, he knew he was powerless, all because of his fallen mate. The one that kept him balanced during their times alone to talk about their emotions. Leonardo was his rock, his yin to his yang when things gotten rough, especially since they found out about not being related.

He along with the other turtles knew that it was a possibility of them not carrying the same blood in their systems, but since they never cared about it at first, they wanted to remain brothers to the very end of their lives. But as time went by, the curiosity grew inside their hearts, especially for the red-headed turtle. He knew deep in his gut that he was different from the rest. Unlike Donatello, his younger and lone brother, Raphael was very into people of the same gender, hell he was also into girls like April. But, he never wanted to admit it out loud he wanted to remain hidden with his feelings locked because of his protector's instincts he always kept within him, and that he figured love was too stupid for him. In the end though, he lost that fight when their 'fearless' leader found about his sexuality in private, by walking in on Raphael's 'private' time in the bathroom by listening to the sounds of his deep churrs and a piece of one of his old bandana rubbing against Raphael's chest.

It was the most embarrassing moment of Raphael's life, but after hours of trying to punch through the harden barrier, Raphael caved in and Leonardo won the fight. Only because the leader of the ninjas didn't leave him be, but stood in place with a concerning gaze in his eye and much to confess as well. Once the door was shut, they learned a lot about each other, not giving a shit if their younger brothers stormed in on them. By the end of that 'special' day, Raphael felt free to be himself, and so did Leonardo. For Leonardo, he softly confessed to being gay, even though there many times he felt in love with their old enemy Karai. When it came down to everything in the room, Leonardo discovered his rightful sexuality when his eternal crush finally kissed him on the lips. It was a test run for the both of them, but it made their worlds spun, their hearts flipping inside of their chests, just waiting to break free to mend together as once. It made them happy that they were finally free to be themselves, to be at peace with themselves and to not never feeling angry like Raphael had for many years.

They were now the same, the perfect yin and yang that Splinter had always envisioned when teaching them the ways of the shinobi. Though now, things were different.

Their family members were broken pieces, scattered throughout the woods their farmhouse was surrounded by, each doing their own thing and wondering if Leonardo was going to wake up for the first time ever in four months. Raphael was stubborn, however, he stayed and hoped even when he was the first to admit that there was no hope for them. He had doubts, but wanted to stay hopeful, for Leonardo's sake. Raphael closed his eyes, whispering his prayers to Leo before he heard the tiny knock on the door.

"Who is it?" Raphael asked tiredly, not opening his eyes.

"Hey Raph, it's me." Michelangelo answered, opening the door wide enough to let him and the tray of food inside the room. "April made dinner so I figured you wanted some." He placed the tray in front of the weary turtle and sat down next to him.

"Oh.. Thanks." Raph whispered, opening his eyes and grabbing the grill cheese sandwich and nibbling on it. "What's up?" Mikey lowered his gaze to the stubs of the bathtub.

"Just bored. Things are too quiet here," Mikey replied, hugging his knees to his chest. "I figured you could use the company since your guest here is sleeping like a baby."

"Oh, well you're welcome to stay here for the night if you want. He's not moving anytime soon and I don't feel like fighting ya."

"I know." They became silent, the breathing between the two blended into a single heat that evaporated into the room for their leader.

"How are the others?" Raph suddenly asked, breaking the silence he grew to despise with a passion. Mikey sighed loudly and leaned back against the wall with his head on his curled up knees. "That bad huh?"

"Everyone's getting tired of keeping up with the norm Raphie, hell even Don won't leave his stupid so-called lab. He thinks what happened with Leo was entirely his fault. I want Leo to wake up, but I also want my family back. I want things to get back to the way they use to be. Is that so bad? Is that so hard to ask in this world of ours?" Mikey back fisted the wall with frustrated grunts, tears flowing down his face when he gave Raphael a pleading look in his baby blue eyes.

Raphael reached out an arm around the younger turtle's shoulder blades and shook him lightly. "It's going to be okay.. Starting tomorrow, we're gonna get everything off their butts and back into motion with training. For Splinter and for Leo." Mikey looked up at Raph and smiled a bit as he wrapped his arms around the older turtle.

"Thanks Raphie. That means a lot to me." Mikey whispered. The protector of the family gave him a once in a lifetime smile of reassurance and stroke Mikey's arm.

"Anytime little bro, anytime."

"Little bro? I thought you weren't gonna call me that anymore."

"Regardless of that DNA bullshit, if I'm mates with Fearless then you're my brother, blood or not."

"Thanks. But, I don't think that's going to help Leo in this case or Donnie. We gotta do something now instead of later."

"That's why I suggested training, but right now, we must rest. It'll be easier for us to kick some shells into place after we rest. Leo will like that." Raphael looked at the sleeping body in the tub in small hopes that he would see movement, but he didn't. Raphael looked down to his younger 'brother' and saw that he fell asleep with his breathing evening out, his face symbolizing an innocent child. With a tired smile, Raphael huddled in his lover's blanket, covering mostly Michelangelo with it before closing his eyes. Slowly letting the silence become his lone lullaby.

x-x

Morning rose, the sun's dimming rays reflected against the opposite wall, Michelangelo was the first to rise up from his slumber since his older brother couldn't do it at this time. He carefully sat up, making sure that Raphael didn't wake up by placing his head on the floor and covering his body with his special blanket. He looked over at the tub, but frowned at it. Leonardo didn't improve overnight like he hoped; it was the same as before. Leonardo sleeping the day and night away. Was it even possible that he was hearing everything that was going on in this farmhouse? Michelangelo wondered in the back of his mind.

The younger turtle walked over to the bathtub and rubbed his hand on his brother's head, few tears falling down on his puffy cheeks.

"Morning Aniki. We miss you, wake up for us okay? Please." Mikey whispered in a small, hopeful tone. He walked over to the door and quietly twisted the knob so he can open it. His baby blue eyes looked towards Raphael's sleeping form again and smiled. "Leo, if you can hear me, do this for me. Don't wake up because I'm telling you too as your little bro. Do it for the one that's been keeping an eye out for you. Yeah he's a pain in the ass, but he's worth the fight to live. We all are, but mostly him. Okay? See you later." Michelangelo closed his mouth, stepped outside of the room with his hand closing the door slowly with the tiny click being the only source of noise.

x-x

Raphael woke to the sound of the bathroom shutting, giving him a mental insight that the younger turtle took off for the day. He sat up, rubbing his emerald eyes before taking his morning glance over to Leonardo. He folded the blanket neatly and placed it next to his stool and photograph before walking over to the tub with his hand reaching to stroke the top of his lover's head.

"Hey.. How you'd sleep? Just kidding. I know how you slept, still are huh? Healing away in silence. I finally got a decent night to sleep, maybe I should let Mikey sleep in here more often huh?" Raphael looked down at the water, examining the multiple scars that were embedded throughout Leonardo's skin. Raphael felt his anger rising once he glanced at the scar that went down from both his lover's shoulders right down to the veins of the wrists respectfully, and the long one on top of his head, almost going over his right eye. Raphael clutched the tub, his knuckles turning blue. Why didn't Leo call for help? When he looked to his peaceful lover, the rage inside turned into despair, realizing it was too late to even wonder about it now. Not long after it, Raphael leaned down to kiss Leo's temple, as it was a custom ritual for him to do before descending down the steps for the day, for Mikey's sake. Otherwise he would've stay here forever if that what it took to be alone with Leonardo.

"Leo, I will kill him. I swear to you. Once you wake up, I'm going after him. Then maybe we can get that quiet life you always wanted. Maybe Splinter will finally be avenged. And maybe you if you've passed on without telling me. I don't know, I hate this shit and I know you do too. But dammit Leo, quit being a scaredy-cat and be the fearless soldier I know you are! Please." Raphael broke down in tears, his body trembling in place.

"Everyone needs you, I frickin' need you. Please my yinny, come back to me. Please!" He punched the tub, going down on his knees, trying to keep his inner world in place inside his growing barrier before it shattered from stress.

Minutes passed and Raphael wiped his tears away, standing up with a grim expression, silently and slowly hoping for a miracle for his lover. He kissed Leonardo's temple one last time before turning around to walk out the door to see his broken family in a solemn silence for the day.


	3. Chapter Two

Hey guys, welcome back to _The Falling Lotus_. Thank you for taking the time to read my story so far, it means a lot to me and I hope you'll enjoy this and other future installments of this story.

 **Warning:** OCC-ness from set characters, AU-ness, graphic language, violence, and sexual content in further chapters. T-Cest (The turtles are not biologically related in this series).

 **Disclaimer:** I don't own anything TMNT related, it rightfully belongs to their creators. I only own Riku, Oshiro, Takuya, Kenji, Hibki, and Minoru. They're the main occs I plan on putting into my TMNT fan fic universe unless stated otherwise. :)

 **Review Replies:**

 ** _Yukio87:_** First off, thank you so much for review this story! It means a lot to me. To answer your question, the pairings I set for my works are final, so like RaphxLeo, they are going to be together in the end of this fic (Mainly because I love that pairing too and I agree with how you feel about their relationship haha). I just need to add drama upon drama to make this story exciting I guess. I hope this answers everything for you. :)

* * *

 **Chapter Two**

* * *

Raphael walked down the hallway to the smell of eggs and Canadian bacon being cooked by the youngest turtle in the kitchen. He shot quick glances at the cracked doors and saw that no one, including Donatello were in their respectful rooms. With a heavy sigh, Raphael walked down the stairs and went straight towards the kitchen, seeing everyone expect for their beloved genius eating in a solemn silence.

"Morning Raph!" Michelangelo cheered, getting a plate ready for him.

"Hey." Raphael muttered as the lone girl gave him a sleepy smile and Casey nodding his head once while wolfing down his food. "Where's Don?"

"He's out in the barn again. He claimed that the medicine for Leo is almost done." April answered as she took a sip of her tea. Michelangelo set the plate down in front of his 'brother' as soon he took a sit next to him to eat his own food.

"Well Donnie better crawl out of that lab because we got some fun stuff planned today!" Michelangelo stated as he took a huge bite of his breakfast. April raised her brow and titled her head.

"What do you have in mind Mikey? she asked, turning her head to glare at Casey who kept chewing his food with a loudness that could wake up the animals outside.

Casey looked at April and stopped eating, swallowing the food down his throat before speaking. "Ehh sorry Red," he said before looking at the orange branded turtle with a bored expression on his face. "What's the plan Mikey?"

"Raph suggested training for a while, but maybe in a couple of days we can take a hike in the woods or something like that." Mikey answered, finishing up his food before leaning back against the chair.

"That sounds like a great idea Mikey, but how are we going to convince Donnie to go and who is going to watch over Leo?" We can't exactly leave him alone like that." April questioned as she stood up to take the dishes to the sink.

"Aww we'll be fine Red, besides maybe it would speed up time and Leo will make his grand entrance when we return from the hike." Casey replied, agreeing with the youngest out of the group. "Besides, I wanna start training again, I'm getting too bored just laying around waiting for the boss to wake his butt up." He eyed his best friend, flinching at the dark glare he was receiving at the given moment.

Michelangelo sighed and glanced over at his 'brother', feeling defeated with the idea. Raphael looked towards Michelangelo and smacked the table with both hands, his chair falling back on the wooden floor. "I say we do it. Leo will be alright and won't go far tomorrow for the hike. Plus, a little training won't kill us today since we've been cooped up in this hellhole for four months." Their protector stated firmly, "The only thing that would be annoying to do is-"

"To get Don out of the barn." April finished, drying off the last plate from the sink.

"Yeah, but oh well. Case and I will handle Donnie while you guys get started with sparring." Raphael replied, picking up the chair he knocked over. Afterwards, Raphael motioned the lone male human to pile his ass off his chair and out the door with his gear. April and Michelangelo watched the door opening and shutting before they could even blink. Moments later, they hurried along to get their own belongings for the training session.

x-x

In the barn, Donatello was shaking the tube of the special medicine he prepared for their fallen leader. It took him the majority of their time in the farmhouse, but the young genius knew that in his heart that this particular formula was the best treatment for Leonardo to get his recovery jump started before heading back to the city.

"Yo D, let's go! We got some training to do!" Casey voiced boomed within the thin walls. Donatello's body jolted in place, the small tube almost spilling all over the table, but in a lucky attempt, the genius was able to save it.

"Casey! What the heck is wrong with you?! I'm in the middle of an important experiment." Donatello hissed, throwing his bo staff at the human as he was closing the door behind him. Raphael rolled his eyes and grabbed the tube from his brother before it gotten destroyed.

"He's just calling you to get outside. We're gonna start training again to pass time." Raphael muttered, placing the tube in its rightful place.

"But I can't train Raph, I have to finish the medicine." Donnie explained, grabbing the other materials to resume his experiment.

"We know D, but what happened wasn't your fault. Leo would want you to understand that and will want you take a break from working so damn hard. Want you around, not cooped up in the barn twenty four/seven."

Donatello sighed heavily and stirred the liquid contents with gentle flicks of the wrist. "Just give me a few more minutes, then I'll let it rest here till we're done training okay? I really want to finish it."

"Then I'll stand here till you're done." Raphael ordered, looking at Casey. He gave his best friend a motion with his hands to train without them. Casey shrugged his shoulder lazily and walked out of the barn without a word.

"Okay, so if I'm right, this medicine is going to heal his internal wounds. Considering I couldn't really give him a full examination, this well very be the only chance we'll get to healing him to normal capacity in no time." Donnie mentioned, pouring a dash of another tube of fluids. Raphael silently nodded and crossed his arms on his chest. His eyes looking at the bright green goo that laid still on his brother's lab table.

"Do you think he'll ever wake up?" Raphael suddenly asked, feeling doubt growing heavily on his shoulders as he looked away to state at the barn door. Donatello looked at his older brother and nodded.

"He has too Raph, he wouldn't give up on us so easily."

"I know that, but think about it. He's been asleep for four months now... If he was getting any better, he would've woken up by now or at least when we first placed his body in the tub."

"But with that water Raph, Leo's body is healing faster than a normal person would when in a coma. His spirit could also be mending everything together and you know how long that takes. Remember when Splinter healed you?"

"Yeah, but I still scarred up in the process." Raphael stroked his lightning shaped scar with a simple touch. "All I'm saying is maybe we're in over our heads with this idea. I mean, Leo's our leader and I don't want to give up on him, but what if we're keeping a corpse in that tub? What if we're just keeping him from dying peacefully because we're being fucking selfish for wanting him to live Donnie? He deserves more than what we're giving him you know?"

Donatello quickly rose up from his chair and jabbed his brother in the jaw. "How the fuck can you say that to me when I've been the one struggling with making this stupid medicine for him since the moment we arrived here?!"

Raphael stumbled back, readjusting his jaw back into place. "I just want Leo to have peace from the constant pain and it sickens me to see this shit happening to him. You see how everyone is acting lately, especially you. You're mopey and dead to us 'cause you got this strange idea that this whole shit is your fault. But it's not Don, at all. Leo and Splinter wouldn't want you to think this way." Raphael looked away from the genius's glare, his body trembling with the tears that wanted to pour out from the growing frustration he held in for so long.

Donatello came up to him and punched him twice more in the same spot. By the fourth punch, the older one blocked it with ease.

"You are so frickin' smug Raphael. You are the protector of this family, not a child like Mikey. You begged me to make this medicine for him after giving us the grand speech of not wanting to give up on him. And now out of nowhere, you want to say this to me? How dare you Raphael."

"I only want what's best for him and everyone else. He's been sleeping in that fuckin' tub for four months Don! Four long ass months. I'm tired of watching him suffer. I'm tired of watching everyone else suffer as well. If he's still alive in that tub, then so be it. But, if he doesn't give change by the first of the next month, then I want to give him a proper burial and you cannot stop me. Got it?"

"But Mikey will. You're not Leonardo's brother."

"And either are you." Raphael countered with a shadowy glare in his eye. "I know you thought of this too, so don't judge me." Donatello rolled his eyes and looked right at his paperwork.

"I did, but you and Mikey were so desperate for a cure for Leonardo, I had to do this. So I don't want to hear anymore whining or else I'm leaving this farmhouse without you all. So, let me get back to work." Donnie muttered bitterly. Raphael's growls rumbled throughout the barn. The young genius didn't flinch when the sounds of wood breaking echoed in his eardrums. He looked to Raphael's exterior and saw the dark circles underneath in his brother's eyes growing noticeable by the second.

The Purple ninja stood up and placed his hand on his older brother's shoulder. "I'm sorry for snapping at you Raphael, but even I'm growing tired of the wait.. Leo will wake up.. Give him time."

"But how much time Donnie? He's been sleeping for so long while the city is dying and Splinter is practically gone. Why can't things go back to normal?"

"They will soon. I can't promise it, but they will." Donatello squeezed his hand as Raphael delivered a quick nod. The young genius then turned back to the table to add in a few things to the test tube.

"I know." Raphael whispered, crossing his arms. He watched his younger brother hard at work, the tongue sticking out of habit before looking through the crack of the door to watch the others jumping around during their training.

"By Sigmund Freud I did it! The medicine is complete!" Donatello suddenly burst out right as he rushed over to bear hug the protector of the family. The red-branded ninja groaned at the touch, but let the young turtle have his moment.

"So will it work or not?" Raphael asked as he lightly pushed the younger turtle away. His brother answered with two quick nods, pouring the contents into a bottle with a "Leo's" label taped in the center.

"When he wakes up it will, but I'll make up a IV for him after training so his body can start getting use to him. With this medicine, it will help Leo's internal wounds heal faster than the water did in the tub. We can move him to the spare room once I get the IV pole set up. I can't wait to tell the others."

Raphael gave Donatello a rare smile and wrapped one arm around his brother's shoulders as he lead them out the door. "I'm proud of you little bro, there really is a brain underneath that skull of yours huh?"

"Oh hush you." Donatello smiled lightly with the medicine in hand. Raphael pushed the door opened with the sun's mid-morning rays hitting them in the right direction.


End file.
